Logan (Hugh Jackman) is in jail in Canada, searching for answers about his past, when he's visited by Zen, a mysterious Japanese man that offers him the answers he looks for it, in exchange, he accompanies him on a trip to Japan.

There, Logan meets Yukio, a skilled martial artist that acts as his bodyguard, and falls in love with Mariko Yashida, daughter of Shingen Yashida, the leader of Yakuza. Mariko is being forced to marry the corrupt Minister of Justice Noburo Moro by her father, in hopes of giving Yakuza complete control over the city.

Shingen's father was the leader of the Hand, a secret society of Ninjas. Instead of naming Shingen his replacement, he commited suicide and left the Hand leaderless in hopes that one of its members, Zen, would convince Logan to take that position.

Meanwhile, Logan is targed by Kenuchio Harada, Shingen's illegitimate son and a mutant with a electrified Silver Samurai armor that plans to kill Logan in order to restore Mariko's honor, finally being accepted into his father's clan. Kenuchio's girlfriend, Viper, is Moro's secretary and a member of the Hand, whereas Yukio, with whom Logan has a unresolved sexual attraction, secretly answers to Yakuza and Shingen, and is divided between who to follow: Logan or Shingen.